3. Liga 2008/09 Liga
| # | Team | Sp | S | U | N | Tore | Diff | Pkt | Form | Tend. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1. FC Union Berlin | 35 | 21 | 11 | 3 | 55:19 | +36 | 74:20 | – | |
| 2 | SC Paderborn 07 | 35 | 18 | 8 | 9 | 59:36 | +23 | 62:35 | – | |
| 3 | SpVgg Unterhaching | 35 | 18 | 7 | 10 | 50:41 | +9 | 61:37 | – | |
| 4 | Fortuna Düsseldorf | 35 | 17 | 9 | 9 | 50:32 | +18 | 60:36 | – | |
| 5 | FC Bayern München II | 35 | 13 | 15 | 7 | 48:34 | +14 | 54:36 | ▲ | |
| 6 | BSV Kickers Emden | 35 | 14 | 10 | 11 | 40:41 | -1 | 52:43 | ▼ | |
| 7 | Kickers Offenbach | 35 | 12 | 13 | 10 | 38:33 | +5 | 49:43 | – | |
| 8 | VfB Stuttgart II | 35 | 13 | 9 | 13 | 57:44 | +13 | 48:48 | ▲ | |
| 9 | SV Sandhausen | 35 | 12 | 11 | 12 | 51:45 | +6 | 47:47 | ▼ | |
| 10 | FC Erzgebirge Aue | 35 | 12 | 11 | 12 | 42:40 | +2 | 47:47 | – | |
| 11 | FC Rot-Weiß Erfurt | 35 | 13 | 8 | 14 | 42:44 | -2 | 47:50 | ▼ | |
| 12 | SG Dynamo Dresden | 35 | 12 | 9 | 14 | 40:42 | -2 | 45:51 | ▲ | |
| 13 | Eintracht Braunschweig | 35 | 12 | 8 | 15 | 43:44 | -1 | 44:53 | ▼ | |
| 14 | Wuppertaler SV | 35 | 10 | 11 | 14 | 33:41 | -8 | 41:53 | ▲ | |
| 15 | SSV Jahn Regensburg | 35 | 9 | 12 | 14 | 32:48 | -16 | 39:54 | ▼ | |
| 16 | SV Wacker Burghausen | 35 | 9 | 10 | 16 | 37:55 | -18 | 37:58 | ▲ | |
| 17 | FC Carl Zeiss Jena | 35 | 9 | 10 | 16 | 35:53 | -18 | 37:58 | ▼ | |
| 18 | VfR Aalen | 35 | 7 | 15 | 13 | 32:55 | -23 | 36:54 | – | |
| 19 | SV Werder Bremen II | 35 | 8 | 10 | 17 | 45:57 | -12 | 34:61 | – | |
| 20 | SV Stuttgarter Kickers | 35 | 7 | 11 | 17 | 37:62 | -25 | 32:62 | – |